Variant report

Variant	rs11249658
Chromosome Location	chr5:179114462-179114463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179113109..179114962-chr5:179124338..179126802,2	MCF-7	breast:
2	chr5:179105459..179107378-chr5:179114144..179116210,2	K562	blood:
3	chr5:179114401..179118460-chr5:179124175..179127183,5	K562	blood:
4	chr5:179106241..179110085-chr5:179114394..179117235,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225051	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000204659	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11249655	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249656	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249657	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11747219	0.96[YRI][hapmap]
rs11749559	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11750523	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12188238	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515399	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12518476	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28674071	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28846185	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34646062	0.81[JPT][hapmap]
rs55702506	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56159807	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60216315	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62406697	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62406698	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67484565	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6879412	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7700649	0.96[YRI][hapmap]
rs7719302	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637934	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9637935	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9763971	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11249658	CLTB	cis	parietal	SCAN
rs11249658	PROP1	cis	parietal	SCAN
rs11249658	GRM6	cis	cerebellum	SCAN
rs11249658	CANX	cis	parietal	SCAN
rs11249658	MAPK9	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179106400-179118200	Weak transcription	Right Ventricle	heart
2	chr5:179106600-179124200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:179106600-179124800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:179106800-179123000	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:179107400-179121400	Weak transcription	Primary B cells from cord blood	blood
6	chr5:179107600-179117600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:179107600-179119600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:179107600-179123200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:179107600-179123200	Weak transcription	Fetal Thymus	thymus
10	chr5:179107600-179123400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:179108000-179115600	Weak transcription	Brain Substantia Nigra	brain
12	chr5:179108400-179123000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:179108600-179123600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:179113800-179118200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:179114000-179123000	Weak transcription	HepG2	liver

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